LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8509989 2.8509989 2.8509989 Created orthogonal box = (0.0000000 -30.306534 0.0000000) to (30.306534 30.306534 2.8509989) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0229912 4.0229912 2.8509989 Created 226 atoms using lattice units in orthogonal box = (0.0000000 -30.306534 0.0000000) to (30.306534 30.306534 2.8509989) create_atoms CPU = 0.001 seconds 226 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0229912 4.0229912 2.8509989 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -30.306534 0.0000000) to (30.306534 30.306534 2.8509989) create_atoms CPU = 0.001 seconds 227 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 18 1 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 453 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_262519520678_001#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1622.3219 0 -1622.3219 163075.78 60 0 -1932.1188 0 -1932.1188 10817.059 Loop time of 7.29812 on 1 procs for 60 steps with 453 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1622.32188266692 -1932.11709399128 -1932.11876644409 Force two-norm initial, final = 527.33605 0.14972392 Force max component initial, final = 194.27241 0.041276410 Final line search alpha, max atom move = 1.0000000 0.041276410 Iterations, force evaluations = 60 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.2774 | 7.2774 | 7.2774 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011967 | 0.011967 | 0.011967 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008777 | | | 0.12 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4437.00 ave 4437 max 4437 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61062.0 ave 61062 max 61062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61062 Ave neighs/atom = 134.79470 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.468 | 4.468 | 4.468 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -1932.1188 0 -1932.1188 10817.059 5237.2051 76 0 -1932.746 0 -1932.746 -0.36162824 5268.1747 Loop time of 1.13999 on 1 procs for 16 steps with 453 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1932.11876644409 -1932.74429364116 -1932.74595056769 Force two-norm initial, final = 93.898784 0.36074909 Force max component initial, final = 92.927626 0.074000698 Final line search alpha, max atom move = 0.00040921306 3.0282052e-05 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1325 | 1.1325 | 1.1325 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0017626 | 0.0017626 | 0.0017626 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005763 | | | 0.51 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4449.00 ave 4449 max 4449 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58618.0 ave 58618 max 58618 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58618 Ave neighs/atom = 129.39956 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1932.746 0 -1932.746 -0.36162824 Loop time of 7.036e-06 on 1 procs for 0 steps with 453 atoms 184.8% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.036e-06 | | |100.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4419.00 ave 4419 max 4419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57640.0 ave 57640 max 57640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57640 Ave neighs/atom = 127.24062 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.605 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -1932.746 -1932.746 30.416226 61.407125 2.8205648 -0.36162824 -0.36162824 -5.4912334 -5.2003865 9.6067352 2.37914 356.6003 Loop time of 6.886e-06 on 1 procs for 0 steps with 453 atoms 275.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.886e-06 | | |100.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4419.00 ave 4419 max 4419 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28820.0 ave 28820 max 28820 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 57640.0 ave 57640 max 57640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57640 Ave neighs/atom = 127.24062 Neighbor list builds = 0 Dangerous builds = 0 453 -1932.74595056769 eV 2.37913996799904 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09